AMBER Archive (2009)

Subject: Re: [AMBER] implicit and explicit simulation: salt effect

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Jan 10 2009 - 10:23:08 CST

On Sat, Jan 10, 2009, Catein Catherine wrote:
>
> I would like to study the salt effect for the binding
> of a neutral drug with DNA from 0M to 0.5 M of salt in a QUALITATIVE
> manner. It seems to me that I can do the GB simulation with salt effect
> considered. According to amber website, it seems to me that it is not
> a problem at all to do the simulation up to 0.2M salt. What about up
> to 0.5 M of salt for qualitative analysis?

My view is that qualitative effects are probably OK with this level of
salt. But you might want to consider taking snapshots of drug-DNA
conformations and analyzing them with PB instead of GB. And, as already
noted in this thread, none of these theories accounts for specific
interactions that might occur with a specific salt.

> If I should only do the
> analysis with explicit solvent, how can I incorporate salt effects in
> the simulation? what is the command line should I used?

You just figure out how many ions you need to get to the desired
concentration, then use the addIons command in leap to get them in
there. Be sure to do lots of equilibration, since it may take a while
for the ion placement to relax from its starting point. Also, do lots
of sampling, since averaging over ion positions can be tedious. (Of
course, the reason for having implicit solvent models in the first place
is to avoid such difficulties of explicit solvent.)

Also worth noting: only the original HCT GB (igb=1) has had much
characterization with DNA. This doesn't mean the other variants are
worse, but I don't think they have been tested as much.

If you do opt for explicit solvent calculations, be sure to look at
issues of ion parameterization:

%A I.S. Joung
%A T.E. Cheatham, III
%T Determination of alkali and halide monovalent ion parameters for use
in explicitly solvated biomolecular simulations
%J J. Phys. Chem. B
%V 112
%P 9020-9041
%D 2008

...good luck...dac

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